Improving Microbial Genome Annotations in an Integrated Database Context

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Chen, I Min A ^a   Markowitz, Victor M ^a   Chu, Ken ^a   Anderson, Iain ^b   Mavromatis, Konstantinos ^b   Kyrpides, Nikos C ^b   Ivanova, Natalia N ^b  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b DOE JOINT GENOME INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; CLASSIFICATION ALGORITHM; DATA ANALYSIS; GENE CLUSTER; GENE SEQUENCE; GENETIC DATABASE; GENETIC TRAIT; GENOME ANALYSIS; NONHUMAN; ORTHOLOGY; PHENOTYPE; PREDICTION; PROCESS DEVELOPMENT; SEQUENCE HOMOLOGY; SYSTEM ANALYSIS; VALIDATION PROCESS;

DATABASES, GENETIC; MICROBIOLOGY; MOLECULAR SEQUENCE ANNOTATION; PHENOTYPE;

EID: 84873739550     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0054859     Document Type: Article

References (24)

1. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Research 33(17): 5691-5702.
2. Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, et al. (2010) MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Research 38: D396-D400.
3. Gillespie JJ, Wattam AR, Cammer SA, Gabbard JL, Shukla MP, et al. (2011) PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect Immun 79(11): 4286-98.
4. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M, (2012) KEGG for integration and interpretation of large-scale molecular datasets. Nucleic Acids Research 40: D109-114.
5. Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, et al. (2008) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Research 36: D623-D631.
6. Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, et al. (2009) MicroScope: a platform for microbial genome annotation and comparative genomics. Database (Oxford): bap021.
7. Wilke A, Harrison T, Wilkening J, Field D, Glass EM, et al. (2012) The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinformatics 13: 141.
8. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41.
9. Punta M, Coggill PC, Ebenhardt RY, Mistry J, Tate J, et al. (2012) The Pfam protein families database. Nucleic Acids Research 40: D290-D301.
10. Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, et al. (2007) TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Research 35: D260-D264.
11. Datta RS, Meacham C, Samad B, Neyer C, Sjolander K, (2009) Berkeley PHOG: PhyloFacts orthology group prediction web server. Nucleic Acids Research 37: W84-W89.
12. Altenhoff AM, Dessimoz C, (2009) Phylogentic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol 5(1): e1000262.
13. Mazin PV, Gelfand MS, Mironov AA, Rakhmaninova AB, Rubinov AR, et al. (2010) An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies. Algorithms Mol Biol 5: 29.
14. Markowitz VM, Mavromatis K, Ivanova NN, Chen IMA, Chu K, et al. (2009) IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25(17): 2271-2278.
15. Markowitz VM, Chen IMA, Palaniappan K, Chu K, Szeto E, et al. (2012) IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Research 40: D11-D122.
16. Mavromatis K, Ivanova NN, Chen IMA, Szeto E, Markowitz VM, et al. (2009) The DOE-JGI standard operating procedure for the annotations of microbial genomes. SIGS 1(1): 68-71.
17. Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, et al. (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Research 40: D306-D312.
18. Markowitz VM, Kyrpides NC, (2007) Comparative genome analysis in the integrated microbial genomes (IMG) system. Methods Mol Biol 395: 35-56.
19. Mavromatis K, Chu K, Ivanova NN, Hooper SD, Markowitz VM, et al. (2009) Gene context analysis in the context of the Integrated Microbial Genomes (IMG) data management system. PLoS ONE 4(11): e7979.
20. Selkov Jr E, Grechkin Y, Mikhailova N, Selkov E, (1998) MPW: the metabolic pathways database. Nucleic Acids Research 26(1): 43-45.
21. Vassoliou Y, (1979) Null values in database management - a denotational semantics approach. ACM SIGMOD Inter. Symp. on Management of Data 35: 162-169.
22. Pagani I, Liolios K, Jansson J, Chen IMA, Smironova T, et al. (2012) The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Research 40: D571-D579.
23. DeJongh M, Formsma K, Boillot P, Gould J, Rycenga M, et al. (2007) Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics 8: 139.
24. Ishoey T, Woyke T, Stepanauska R, Novotny M, Lasken RS, (2008) Genomic sequencing of single microbial cells from environmental samples. Curr Opinion Microbiol 11(3): 198-204.